kedro.extras.datasets.biosequence.BioSequenceDataSet

class kedro.extras.datasets.biosequence.BioSequenceDataSet(filepath, load_args=None, save_args=None, credentials=None, fs_args=None)[source]

Bases: kedro.io.core.AbstractDataSet

BioSequenceDataSet loads and saves data to a sequence file.

Example:

from kedro.extras.datasets.biosequence import BioSequenceDataSet
from io import StringIO
from Bio import SeqIO

data = ">Alpha\nACCGGATGTA\n>Beta\nAGGCTCGGTTA\n"
raw_data = []
for record in SeqIO.parse(StringIO(data), "fasta"):
    raw_data.append(record)

data_set = BioSequenceDataSet(filepath="ls_orchid.fasta",
                              load_args={"format": "fasta"},
                              save_args={"format": "fasta"})
data_set.save(raw_data)
sequence_list = data_set.load()

assert raw_data[0].id == sequence_list[0].id
assert raw_data[0].seq == sequence_list[0].seq

Attributes

BioSequenceDataSet.DEFAULT_LOAD_ARGS

BioSequenceDataSet.DEFAULT_SAVE_ARGS

Methods

BioSequenceDataSet.exists()

Checks whether a data set’s output already exists by calling the provided _exists() method.

BioSequenceDataSet.from_config(name, config)

Create a data set instance using the configuration provided.

BioSequenceDataSet.invalidate_cache()

Invalidate underlying filesystem caches.

BioSequenceDataSet.load()

Loads data by delegation to the provided load method.

BioSequenceDataSet.release()

Release any cached data.

BioSequenceDataSet.save(data)

Saves data by delegation to the provided save method.

DEFAULT_LOAD_ARGS: Dict[str, Any] = {}
DEFAULT_SAVE_ARGS: Dict[str, Any] = {}
__init__(filepath, load_args=None, save_args=None, credentials=None, fs_args=None)[source]

Creates a new instance of BioSequenceDataSet pointing to a concrete filepath.

Parameters
  • filepath (str) – Filepath in POSIX format to sequence file prefixed with a protocol like s3://. If prefix is not provided, file protocol (local filesystem) will be used. The prefix should be any protocol supported by fsspec.

  • load_args (Optional[Dict[str, Any]]) – Options for parsing sequence files by Biopython SeqIO.parse().

  • save_args (Optional[Dict[str, Any]]) – file format supported by Biopython SeqIO.write(). E.g. {“format”: “fasta”}.

  • credentials (Optional[Dict[str, Any]]) – Credentials required to get access to the underlying filesystem. E.g. for GCSFileSystem it should look like {“token”: None}.

  • fs_args (Optional[Dict[str, Any]]) – Extra arguments to pass into underlying filesystem class constructor (e.g. {“project”: “my-project”} for GCSFileSystem), as well as to pass to the filesystem’s open method through nested keys open_args_load and open_args_save. Here you can find all available arguments for open: https://filesystem-spec.readthedocs.io/en/latest/api.html#fsspec.spec.AbstractFileSystem.open All defaults are preserved, except mode, which is set to r when loading and to w when saving.

Note: Here you can find all supported file formats: https://biopython.org/wiki/SeqIO

exists()

Checks whether a data set’s output already exists by calling the provided _exists() method.

Return type

bool

Returns

Flag indicating whether the output already exists.

Raises

DataSetError – when underlying exists method raises error.

classmethod from_config(name, config, load_version=None, save_version=None)

Create a data set instance using the configuration provided.

Parameters
  • name (str) – Data set name.

  • config (Dict[str, Any]) – Data set config dictionary.

  • load_version (Optional[str]) – Version string to be used for load operation if the data set is versioned. Has no effect on the data set if versioning was not enabled.

  • save_version (Optional[str]) – Version string to be used for save operation if the data set is versioned. Has no effect on the data set if versioning was not enabled.

Return type

AbstractDataSet

Returns

An instance of an AbstractDataSet subclass.

Raises

DataSetError – When the function fails to create the data set from its config.

invalidate_cache()[source]

Invalidate underlying filesystem caches.

Return type

None

load()

Loads data by delegation to the provided load method.

Return type

Any

Returns

Data returned by the provided load method.

Raises

DataSetError – When underlying load method raises error.

release()

Release any cached data.

Raises

DataSetError – when underlying release method raises error.

Return type

None

save(data)

Saves data by delegation to the provided save method.

Parameters

data (Any) – the value to be saved by provided save method.

Raises

DataSetError – when underlying save method raises error.

Return type

None